jalview

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Commits this week: 7
Total Committers: 73
Last Commit:
Commits this week: 7

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Monday 07 Jun 2021
9:32 am

Arnaud Gucciardi

JAL-3929_spike minor changes

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    • -0
    • +4
    /src/jalview/ws/dbsources/TDBeacons.java
    • -1
    • +1
    /test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java
9:32 am

Arnaud Gucciardi

JAL-3829_spike minor changes

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    • -0
    • +4
    /src/jalview/ws/dbsources/TDBeacons.java
    • -1
    • +1
    /test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java
Wednesday 12 May 2021
7:33 pm

Mateusz Warowny

Revert "Merge branch 'bug/JAL-3807_jpred-with-slivka' into alpha/JAL-3066_Jalview_212_slivka-integration"

This reverts commit 95f4ae66fbaecbbdc1c3ab3c6c9c611a3a9a3e46, reversing

changes made to bc7c2cf5500c5a4124a69ef8e7b1374d8997558f.

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    • -16
    • +0
    /src/jalview/ws/api/JPredServiceI.java
    • -6
    • +1
    /src/jalview/ws/api/ServiceWithParameters.java
    • -69
    • +0
    /src/jalview/ws/jws2/JPredClient.java
    • -406
    • +0
    /src/jalview/ws/jws2/JPredThread.java
    • -1
    • +1
    /src/jalview/ws/jws2/jabaws2/Jws2Instance.java
    • -96
    • +0
    /src/jalview/ws/slivkaws/SlivkaJPredServiceInstance.java
    • -6
    • +18
    /src/jalview/ws/slivkaws/SlivkaMsaServiceInstance.java
    • -1
    • +1
    /src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java
    • -28
    • +12
    /src/jalview/ws/slivkaws/SlivkaWSInstance.java
Monday 26 Apr 2021
8:00 pm

Ben Soares

JAL-3248 Moved old README to doc/old_README and put pointers in new README for deskopt application building and JalviewJS building

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    • -71
    • +4
    /README
    • -0
    • +72
    /doc/old_README
6:27 pm

Ben Soares

JAL-3248 Archived old README. Added new README to point user to doc/building.md

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    • -45
    • +1
    /README
    • -0
    • +47
    /doc/old_ant_build_README
5:56 pm

Ben Soares

JAL-3743 Fixed NullPointerExceptions happening with linkCheck task when gradle >= 6.6

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    • -3
    • +2
    /build.gradle
5:56 pm

Ben Soares

JAL-3743 JAL-3745 Fixed NullPointerExceptions happening with linkCheck and jalviewjsTranspile tasks when gradle >= 6.6

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    • -5
    • +4
    /build.gradle
5:56 pm

Ben Soares

JAL-3743 JAL-3745 Fixed NullPointerExceptions happening with linkCheck and jalviewjsTranspile tasks when gradle >= 6.6

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    • -5
    • +4
    /build.gradle
Thursday 22 Apr 2021
6:33 pm

Ben Soares

JAL-4014 4 gecos colour schemes added

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    • -0
    • +64
    /src/jalview/schemes/BlossomColourScheme.java
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    • +64
    /src/jalview/schemes/FlowerColourScheme.java
    • -0
    • +4
    /src/jalview/schemes/JalviewColourScheme.java
    • -0
    • +64
    /src/jalview/schemes/OceanColourScheme.java
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    • +119
    /src/jalview/schemes/ResidueProperties.java
    • -0
    • +64
    /src/jalview/schemes/SunsetColourScheme.java
6:33 pm

Ben Soares

4 gecos colour schemes added

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    • -0
    • +64
    /src/jalview/schemes/BlossomColourScheme.java
    • -0
    • +64
    /src/jalview/schemes/FlowerColourScheme.java
    • -0
    • +4
    /src/jalview/schemes/JalviewColourScheme.java
    • -0
    • +64
    /src/jalview/schemes/OceanColourScheme.java
    • -3
    • +123
    /src/jalview/schemes/ResidueProperties.java
    • -0
    • +64
    /src/jalview/schemes/SunsetColourScheme.java
3:20 pm

Ben Soares

JAL-3833 Allow setHiDPI and setHiDPIScale to work more usefully in real life

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    • -2
    • +17
    /src/jalview/bin/HiDPISetting.java
Monday 19 Apr 2021
4:37 pm

Ben Soares

JAL-3833 cap the scaling used by HiDPISetting for incorrect DPI values or incorrect height/width values

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    • -0
    • +10
    /src/jalview/bin/HiDPISetting.java
Sunday 18 Apr 2021
8:31 pm

Ben Soares

JAL-3833 cap the scaling used by HiDPISetting for incorrect DPI values or incorrect height/width values

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    • -0
    • +10
    /src/jalview/bin/HiDPISetting.java
Tuesday 13 Apr 2021
5:40 pm

Ben Soares

JAL-3830 Improved jalview.bat to find either pwsh.exe or powershell.exe, and give better messages to the user

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    • -3
    • +49
    /utils/getdown/bin/jalview.bat
Monday 12 Apr 2021
3:05 pm

Arnaud Gucciardi

JAL-3832 Gui working, with 3DBeacons parameters

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    • -3
    • +3
    /resources/fts/tdbeacons_data_columns.txt
    • -2
    • +4
    /src/jalview/fts/core/FTSDataColumnPreferences.java
    • -11
    • +14
    /test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java
3:05 pm

Arnaud Gucciardi

JAL-3832 Gui working, with 3DBeacons parameters

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    • -3
    • +3
    /resources/fts/tdbeacons_data_columns.txt
    • -2
    • +4
    /src/jalview/fts/core/FTSDataColumnPreferences.java
    • -11
    • +14
    /test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java
9:17 am

Arnaud Gucciardi

Merge branch 'arnaud/develop' into arnaud/JAL-3929_spike, to insert the previous changes

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9:17 am

Arnaud Gucciardi

Merge branch 'arnaud/develop' into arnaud/JAL-3929_spike, to insert the previous changes

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Tuesday 06 Apr 2021
3:23 pm

Jim Procter

JAL-3929 forgot to add in the dummy 3d-beacons db proxy

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    • -0
    • +521
    /src/jalview/ws/dbsources/TDBeacons.java
3:23 pm

Jim Procter

JAL-3829 forgot to add in the dummy 3d-beacons db proxy

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    • -0
    • +521
    /src/jalview/ws/dbsources/TDBeacons.java
3:04 pm

Jim Procter

JAL-3832 dummy 3d-beacons database client and code to create the TDBeaconsFTSPanel via the sequence fetcher dropdown menu

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    • -0
    • +6
    /src/jalview/gui/SequenceFetcher.java
    • -0
    • +2
    /src/jalview/ws/SequenceFetcher.java
2:25 pm

Arnaud Gucciardi

JAL-3829 more testing wit tdbeacons data columns and FTSclient

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    • +4
    /resources/fts/tdbeacons_data_columns.txt
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    • +2
    /src/jalview/fts/service/pdb/PDBFTSRestClient.java
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    /src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
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    /test/jalview/fts/service/pdb/PDBFTSRestClientTest.java
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    /test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java
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    • +7
    /test/jalview/gui/StructureChooserTest.java
Thursday 01 Apr 2021
2:28 pm

Arnaud Gucciardi

JAL-3829 attempt to fix my changes to follow the Jira issue

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    • -0
    • +3
    /resources/fts/tdbeacons_data_columns.txt
    • -9
    • +10
    /src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
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    • +3
    /test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java
Wednesday 31 Mar 2021
11:16 pm

Ben Soares

JAL-3830 BAT file wrapper around powershell, so jalview works in command prompt. Added install4j option for installer to add Jalview's bin dir to Path in Windows. Added install4j option to create symlink to bash script to user's local bin (first of ~/bin, ~/.local/bin, ~/local/bin, ~/opt/bin that exists. First two of these usually automatically in PATH).

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    /build.gradle
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    /gradle.properties
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    /utils/getdown/bin/jalview.bat
    • -32
    • +84
    /utils/install4j/install4j8_template.install4j
Tuesday 30 Mar 2021
1:43 am

Ben Soares

JAL-3830 Follow all SymbolicLinks in Windows powershell wrapper

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    • -4
    • +41
    /utils/getdown/bin/jalview.ps1
Monday 29 Mar 2021
1:39 pm

Arnaud Gucciardi

fixed last commit

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    /src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
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    • +2
    /test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java
9:51 am

Arnaud Gucciardi

Request now parses the whole structures, need to fix the result

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    /src/jalview/fts/service/threedbeacons/TDBeaconsFTSPanel.java
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    /src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
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    /test/jalview/fts/service/pdb/PDBFTSPanelTest.java
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    /test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java
Friday 26 Mar 2021
5:30 pm

Ben Soares

JAL-3830 delete channel.props and channel.propsv when uninstalling

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    • -1
    • +11
    /utils/install4j/install4j8_template.install4j
Thursday 25 Mar 2021
7:27 pm

Ben Soares

JAL-3633 new getdown jars

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    • binary
    /getdown/lib/getdown-core.jar
    • binary
    /getdown/lib/getdown-launcher-local.jar
    • binary
    /getdown/lib/getdown-launcher.jar
    • binary
    /j11lib/getdown-core.jar
    • binary
    /j8lib/getdown-core.jar
7:27 pm

Ben Soares

JAL-3633 refactored/simplified LaunchUtils code

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    /getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java
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    /getdown/src/getdown/core/src/main/java/jalview/bin/LaunchUtils.java
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    /getdown/src/getdown/core/src/main/java/jalview/util/ChannelProperties.java
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    /getdown/src/getdown/core/src/main/java/jalview/util/LaunchUtils.java
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    /getdown/src/getdown/launcher/src/main/java/com/threerings/getdown/launcher/ProxyUtil.java
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    /src/jalview/bin/LaunchUtils.java
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    /src/jalview/bin/Launcher.java
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    /src/jalview/util/ChannelProperties.java
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    /src/jalview/util/LaunchUtils.java